FastxOutputStream< Writer > Class Template Reference

#include <genesis/sequence/formats/fastx_output_stream.hpp>

Detailed Description

template<class Writer>
class genesis::sequence::FastxOutputStream< Writer >

Write Fasta or Fastq data, sequentially.

This class allows to write Sequence data to an output target, using Fasta or Fastq format, without the need to have a full SequenceSet containing all Sequences in memory.

Exemplary usage:

auto out_it = FastqOutputStream( utils::to_file( "path/to/out.fastq" ));
while( ... ) {
    Sequence seq = ...
    out_it << seq;
}

See the output target convenience functions utils::to_file(), utils::to_stream(), and utils::to_string() for examples of how to obtain a suitable output target.

Definition at line 57 of file fastx_output_stream.hpp.

Public Member Functions
	FastxOutputStream ()=delete
	FastxOutputStream (self_type &&)=default
	FastxOutputStream (self_type const &)=default
	FastxOutputStream (std::shared_ptr< utils::BaseOutputTarget > target)
	FastxOutputStream (std::shared_ptr< utils::BaseOutputTarget > target, Writer const &writer)
	~FastxOutputStream ()=default
self_type const &	operator<< (Sequence const &sequence) const
self_type &	operator= (self_type &&)=default
self_type &	operator= (self_type const &)=default
std::shared_ptr< utils::BaseOutputTarget >	output_target () const
self_type const &	write (Sequence const &sequence) const
template<typename T = Writer, typename std::enable_if< std::is_same< T, FastqWriter >::value >::type * = nullptr>
self_type const &	write (Sequence const &sequence, std::string const &quality_string) const
	Writer overload for Fastq files where the quality_string is provided instead of taken from the sequence. More...
Writer &	writer ()
	Return the Writer used for this iterator. More...
Writer const &	writer () const

Public Types
using	self_type = FastxOutputStream

Constructor & Destructor Documentation

FastxOutputStream() [1/5]

FastxOutputStream ( )

delete

FastxOutputStream() [2/5]

FastxOutputStream ( std::shared_ptr< utils::BaseOutputTarget >  target )

inlineexplicit

Definition at line 100 of file fastx_output_stream.hpp.

FastxOutputStream() [3/5]

FastxOutputStream ( std::shared_ptr< utils::BaseOutputTarget >  target, Writer const &  writer  )

inline

Definition at line 107 of file fastx_output_stream.hpp.

~FastxOutputStream()

~FastxOutputStream ( )

default

FastxOutputStream() [4/5]

FastxOutputStream ( self_type const &  )

default

FastxOutputStream() [5/5]

FastxOutputStream ( self_type &&  )

default

Member Function Documentation

operator<<()

self_type const& operator<< ( Sequence const &  sequence ) const

inline

Definition at line 127 of file fastx_output_stream.hpp.

operator=() [1/2]

self_type& operator= ( self_type &&  )

default

operator=() [2/2]

self_type& operator= ( self_type const &  )

default

output_target()

std::shared_ptr<utils::BaseOutputTarget> output_target ( ) const

inline

Definition at line 180 of file fastx_output_stream.hpp.

write() [1/2]

self_type const& write ( Sequence const &  sequence ) const

inline

Definition at line 133 of file fastx_output_stream.hpp.

write() [2/2]

self_type const& write ( Sequence const &  sequence, std::string const &  quality_string  ) const

inline

Writer overload for Fastq files where the quality_string is provided instead of taken from the sequence.

Definition at line 147 of file fastx_output_stream.hpp.

writer() [1/2]

Writer& writer ( )

inline

Return the Writer used for this iterator.

Use this to change the settings and writing behaviour of the iterator. See Writer for details.

Definition at line 191 of file fastx_output_stream.hpp.

writer() [2/2]

Writer const& writer ( ) const

inline

Definition at line 196 of file fastx_output_stream.hpp.

Member Typedef Documentation

self_type

using self_type = FastxOutputStream

Definition at line 92 of file fastx_output_stream.hpp.

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The documentation for this class was generated from the following file:

• fastx_output_stream.hpp